It has long been recognized that certain sites within a protein, such as sites in the protein
core or catalytic residues in enzymes, are evolutionarily more conserved than other sites …

Abstract HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source
package for fitting a broad range of evolutionary models to multiple sequence alignments …

The independent emergence late in 2020 of the B. 1.1. 7, B. 1.351, and P. 1 lineages of
SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to …

Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that
have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within …

This review is motivated by the true explosion in the number of recent studies both
develo** and ameliorating probabilistic models of codon evolution. Traditionally …

The evolutionary trajectory of a protein through sequence space is constrained by its
function. Collections of sequence homologs record the outcomes of millions of evolutionary …

In this study, we analyzed full-length SARS-CoV-2 genomes from multiple countries to
determine early trends in the evolutionary dynamics of the novel COVID-19 pandemic …

The RV144 trial demonstrated 31% vaccine efficacy at preventing human immunodeficiency
virus (HIV)-1 infection. Antibodies against the HIV-1 envelope variable loops 1 and 2 (Env …

Identifying the genetic mechanisms of adaptation requires the elucidation of links between
the evolution of DNA sequence, phenotype, and fitness. Convergent evolution can be used …

Distinguishing self from non-self is a fundamental biological challenge. Many pathogens
exploit the challenge of self discrimination by employing mimicry to subvert key cellular …